Is this normal

At step 2.4.2, I-TASSER shows FORTRAN STOP ,but the program is still running.However, after I stop the program and run it again, it shows step 2.4 only,and then step 3.1, the FORTRAN STOP is neglected..........., can this error—— FORTRAN STOP be neglected???
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1. make seq.txt and rmsinp
2.1 run Psi-blast
2.2 run psipred
2.3 run solve
2.3 run solve
2.4 run pairmod
2.4.1 removing homology templates based on real and 1
2.4.2 running pair ................
FORTRAN STOP
3.1 do threading
start threading QQQ
hostname: xnebula
starting time: Tue Nov 8 21:12:27 CST 2011
pwd: /tmp/hlzhang/ITseq.fasta
running Psi-blast .....
running zalign .....
./zalign 7.01 0.55 0.66 1.6 -0.99 0.31 0.19 0 1.0 0.39 0.19
==>1bu5A 1bu5A 21.4022941339032 16.0759207934012
1bu5A 1bu5A 98 98
score_flag=1
ending time: Tue Nov 8 21:44:03 CST 2011
start threading GGGd
hostname: xnebula
starting time: Tue Nov 8 21:44:05 CST 2011
pwd: /tmp/hlzhang/ITseq.fasta
running zalign .....
ending time: Tue Nov 8 21:58:21 CST 2011
start threading GGGf
hostname: xnebula
starting time: Tue Nov 8 21:58:22 CST 2011
pwd: /tmp/hlzhang/ITseq.fasta
running zalign .....
ending time: Tue Nov 8 22:11:50 CST 2011
start threading NNNd
hostname: xnebula
starting time: Tue Nov 8 22:11:51 CST 2011
pwd: /tmp/hlzhang/ITseq.fasta
running zalign .....
ending time: Tue Nov 8 22:19:38 CST 2011
start threading SSSc
hostname: xnebula
starting time: Tue Nov 8 22:19:39 CST 2011
pwd: /tmp/hlzhang/ITseq.fasta
running zalign .....
ending time: Tue Nov 8 22:38:07 CST 2011
3.2 make restraints
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
^C
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1. make seq.txt and rmsinp
2.1 run Psi-blast
2.2 run psipred
2.3 run solve
2.4 run pairmod
3.1 do threading
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